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. 2015 May 21;16(1):400. doi: 10.1186/s12864-015-1570-9

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© Leushkin et al.; licensee BioMed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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((X,Y),Z)/((X,Z),Y)) is a ratio of the number of sites with phylogenetic configuration ((X,Y),Z) to the number of sites with phylogenetic configuration ((X,Z),Y) at distance l to a site with phylogenetic configuration ((X,Y),Z). (A) presents the ratio for strains from the same clade (VKM F-3557, VKM F-4514, VKM F-3808), rooted by VKM F-4246. (B) and (C) presents the ratio for strains from different clades (VKM F-3557, VKM F-4515, VKM F-4246), rooted by VKM F-4519, for synonymous (B) and nonsynonymous (C) sites.